I was using BPMN2 Modeler from Eclipse-Juno release and recently I migrated to Kepler.
When I try to open old Collaboration diagrams, I get this error dialog saying "Multiple elements have same IDs".

Also, if I see the .bpmn2 file, I find there is a new collaboration element added apart from the one existing. And Every time I open the editor, a new collaboration element is again added.

Just thought its worth to mention, that I am extending BPMN2 model and also I am using ext-point "org.eclipse.bpmn2.modeler.runtime" and in this ext-point there is a new attribute "profile" is added under "modelEnablement" element. I went through the samples and made it like below:

You should be aware that we are no longer supporting Juno (more specifically, Graphiti versions older than 0.10.0) as of version 1.0. Since then, a lot of bug fixes and enhancements have been made and the latest version (1.0.1 will be released soon) has quite a few changes in the API as well (as you've already seen). One of these bug fixes addresses the "duplicate ID" problem which was not handled in previous versions of the editor.

As far as the issue you're seeing (new Collaboration is added every time editor is saved) I haven't seen this one before. If possible, can you test with the nightly build and see if this is still an issue? If so, please file a bug report here.